--- mgltools-webservices-1.5.6~rc2+cvs.20111222.orig/debian/rules +++ mgltools-webservices-1.5.6~rc2+cvs.20111222/debian/rules @@ -0,0 +1,16 @@ +#!/usr/bin/make -f +# -*- makefile -*- +# debian/rules for mgltools-volume + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +BRANCH=`cat debian/get-orig-source/current-branch` +RCVERSION=`cat debian/get-orig-source/rc-version` +SRC=WebServicesDIST + +%: + dh $@ --with python2 + +get-orig-source: + ./debian/get-orig-source/get-orig-source $(SRC) $(BRANCH) $(RCVERSION) --- mgltools-webservices-1.5.6~rc2+cvs.20111222.orig/debian/compat +++ mgltools-webservices-1.5.6~rc2+cvs.20111222/debian/compat @@ -0,0 +1 @@ +8 --- mgltools-webservices-1.5.6~rc2+cvs.20111222.orig/debian/copyright +++ mgltools-webservices-1.5.6~rc2+cvs.20111222/debian/copyright @@ -0,0 +1,83 @@ +This package was debianized by Steffen Moeller on +Thu, 10 Jul 2008 00:03:24 +0200 + +It was downloaded from http://mgltools.scripps.edu + +Upstream Authors: + + The main development is performed by the researchers + and developers at the + + Molecular Graphics Laboratory + + led by + + Michael F. Sanner + + with contributions by + + Anna Omelchenko + Sowjanya Karnati + Guillaume Vareille + Daniel Stoffler + Michael F. Sanner + +Copyright: + + The respective authors and the Scripps Research Institute + Copyright 1989-2008 Michael Sanner + +License: + +All files distributed or redistributed in this package are subject +to the here presented license, regardless of the information +that is explicitly stated or omitted in the respective files +themselves. The original copyright holders have made respective +agreements regarding this redistribution. + + + 1. Grant Of Limited License; Software Use Restrictions. The programs + received by you will be used only for NON COMMERCIAL purposes. + This license is issued to you as an individual. + + For COMMERCIAL use done with the software please contact Michel F. + Sanner for details about commercial usage license agreements. + + For any question regarding license agreements, please contact + Michel Sanner: + TSRI, Molecular Biology Department, TCP 26, + 10550 North Torrey Pines Road, La Jolla, CA 92037 + sanner@scripps.edu + tel (858) 784-7742 + fax (858) 784-2341 + + 2. COMMERCIAL USAGE is defined as revenues generating activities. These + include using this software for consulting activities and selling + applications built on top of, or using this software. Scientific + research in an academic environment and teaching are considered + NON COMMERCIAL. + + 3. Copying Restrictions. You will not sell or otherwise distribute commercially + these programs or derivatives to any other party, whether with or without + consideration. + + 4. Ownership of Software. You will not obtain, and will not attempt to + obtain copyright coverage thereon without the express purpose written + consent of The Scripps Research Institute and Dr. Sanner. + + 5. IN NO EVENT SHALL THE AUTHORS OR DISTRIBUTORS BE LIABLE TO ANY PARTY + FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES + ARISING OUT OF THE USE OF THIS SOFTWARE, ITS DOCUMENTATION, OR ANY + DERIVATIVES THEREOF, EVEN IF THE AUTHORS HAVE BEEN ADVISED OF THE + POSSIBILITY OF SUCH DAMAGE. + + 6. THE AUTHORS AND DISTRIBUTORS SPECIFICALLY DISCLAIM ANY WARRANTIES, + INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT. THIS SOFTWARE + IS PROVIDED ON AN "AS IS" BASIS, AND THE AUTHORS AND DISTRIBUTORS HAVE + NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR + MODIFICATIONS. + +The Debian packaging is Copyright (C) 2007-2008, +Steffen Moeller +and is licensed under the GPL, see '/usr/share/common-licenses/GPL'. --- mgltools-webservices-1.5.6~rc2+cvs.20111222.orig/debian/README.Debian +++ mgltools-webservices-1.5.6~rc2+cvs.20111222/debian/README.Debian @@ -0,0 +1,27 @@ +autodocktools and other modules of MGLtools for Debian +====================================================== + +This package aims at providing the complete infrastructure for ligand +screening with Debian Linux. It is part of the MGL (Molecular Graphics +Labs at Scripps) Python tools set for the computational and visual +interaction of protein structures and their ligands. + +The Debian community shall thank Sargis Dallakyan +for his help in easing the compatibility with Debian by accepting our +patches and providing more himself. Also, the leader of the Molecular +Graphics Labs, Prof. Michael Sanner, is thanked for his support. + +Please be continuously reminded that that closer a software gets towards +identifying or further describing functional compounds in medicine, +the harder it is to get access to free (as in beer) solutions. And it +certainly does not get much closer than with the AutoDockToolkit. To +have the AutoDockToolkit with Debian is special and good for the world +as it spawns the development of new drugs. We will need to wait a bit +longer for a DFSG compatible license, though. + +If you are a regular user of this package, your feedback to us +packagers would much appreciated. The packaging is organised +via the Debian-Med alioth project that has its own portal on +http://debian-med.alioth.debian.org. + + -- Steffen Moeller Sun, 20 Jul 2008 00:33:11 +0200 --- mgltools-webservices-1.5.6~rc2+cvs.20111222.orig/debian/changelog +++ mgltools-webservices-1.5.6~rc2+cvs.20111222/debian/changelog @@ -0,0 +1,17 @@ +mgltools-webservices (1.5.6~rc2+cvs.20111222-1) unstable; urgency=low + + * New upstream version. + + -- Steffen Moeller Thu, 22 Dec 2011 17:10:13 +0100 + +mgltools-webservices (1.5.6~rc2+cvs.20110926-1) unstable; urgency=low + + * New upstream version. + + -- Steffen Moeller Tue, 27 Sep 2011 10:58:17 +0200 + +mgltools-webservices (1.5.6~rc1+cvs.20110703-1) unstable; urgency=low + + * Initial release, contributes to closing ITP #458811. + + -- Thorsten Alteholz Fri, 17 Jun 2011 01:20:33 +0200 --- mgltools-webservices-1.5.6~rc2+cvs.20111222.orig/debian/pycompat +++ mgltools-webservices-1.5.6~rc2+cvs.20111222/debian/pycompat @@ -0,0 +1 @@ +2 --- mgltools-webservices-1.5.6~rc2+cvs.20111222.orig/debian/watch +++ mgltools-webservices-1.5.6~rc2+cvs.20111222/debian/watch @@ -0,0 +1,2 @@ +version=3 +http://mgltools.scripps.edu/downloads/.*mgltools_source_([0-9.]+)\.tar\.gz --- mgltools-webservices-1.5.6~rc2+cvs.20111222.orig/debian/mgltools-webservices.lintian-overrides +++ mgltools-webservices-1.5.6~rc2+cvs.20111222/debian/mgltools-webservices.lintian-overrides @@ -0,0 +1,2 @@ +# the license is in debian/copyright but upstream wants to have it there as well +mgltools-webservices: extra-license-file --- mgltools-webservices-1.5.6~rc2+cvs.20111222.orig/debian/README.source +++ mgltools-webservices-1.5.6~rc2+cvs.20111222/debian/README.source @@ -0,0 +1,22 @@ +Any package of the MGLtools suite +================================= + +The URL presented in debian/watch guides to a tar file +as the source distribution of the MGLtools set. That tar file +has a subdirectory MGLPACKS that comprises many tar files +itself, each representing a distinguished Python module. + +For the packaging of the AutoDockTool kit, the maintainers +have decided to package each module individually, to foster +the collaboration between similar applications. + +The maintainers of the Debian package may decide to release +interim version from the upstream CVS source repository, +instead of waiting for an official release by the upstream +developers. + +For further details on how to prepare the source for the +packaging, please refer to +http://svn.debian.org/wsvn/debian-med/trunk/packages/mgltools/BUILD?op=file&rev=0&sc=0 + + -- Steffen Moeller --- mgltools-webservices-1.5.6~rc2+cvs.20111222.orig/debian/control +++ mgltools-webservices-1.5.6~rc2+cvs.20111222/debian/control @@ -0,0 +1,28 @@ +Source: mgltools-webservices +Section: non-free/science +Priority: optional +Maintainer: Debian Med Packaging Team +DM-Upload-Allowed: yes +Uploaders: Steffen Moeller , + Sargis Dallakyan , + Andreas Tille , + Thorsten Alteholz +Build-Depends: debhelper (>= 8),python-all (>= 2.6) +Standards-Version: 3.9.2 +XS-Python-Version: >= 2.5 +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mgltools/webservices/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mgltools/webservices/trunk/ +Homepage: http://mgltools.scripps.edu/ + +Package: mgltools-webservices +XB-Python-Version: ${python:Versions} +Architecture: all +Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends} +Description: webservices for components of autodocktools + This package is part of the mgltools set of Python libraries which + provide an infrastructure for the analysis of protein structures and + their docking of chemical compounds. + . + The web services provide the means for inter-process communication + of different parts of the autodocktools. It is used especially + for the control of workflows addressing in silico screening. --- mgltools-webservices-1.5.6~rc2+cvs.20111222.orig/debian/get-orig-source/rc-version +++ mgltools-webservices-1.5.6~rc2+cvs.20111222/debian/get-orig-source/rc-version @@ -0,0 +1 @@ +~rc2 --- mgltools-webservices-1.5.6~rc2+cvs.20111222.orig/debian/get-orig-source/get-orig-source +++ mgltools-webservices-1.5.6~rc2+cvs.20111222/debian/get-orig-source/get-orig-source @@ -0,0 +1,88 @@ +#!/bin/bash +# +# usage: get-orig-source +# e.g.: get-orig-source VolumeDIST rc-1-5-6 ~rc1 +# +package=$1 +branch=$2 +rcversion=$3 + +REMOTECVSROOT=:pserver:anonymous@mgl1.scripps.edu:2401/opt/cvs +CVS=/usr/bin/cvs +MGLTOOLSCVS=../../mgltools-cvs + +# Expected by svn-buildpackage as 'tarballs' +TARDIR=../tarballs + +PREFIX="mgltools-" +if [ "$package" == "AutoDockToolsDIST" ]; then + PREFIX="" +fi +DEBPACKAGE=$PREFIX`echo $package|sed "s/DIST//g"| tr 'A'-'Z' 'a'-'z'` + +# do some stuff +echo "I: get $package (-> $DEBPACKAGE) from branch $branch" + +loginDone=`grep "$REMOTECVSROOT" ~/.cvspass|wc -l` +if [ "$loginDone" == "0" ]; then + $CVS -d$REMOTECVSROOT login +fi + +if [ -d "$MGLTOOLSCVS" ]; then + echo "I: cvs directory already available" +else + echo "I: create directory '$MGLTOOLSCVS' to store new CVS checkout" + mkdir "$MGLTOOLSCVS" +fi + +if [ -d $MGLTOOLSCVS/$package ]; then + echo "I: ... checkout already done" + if [ -r "$MGLTOOLSCVS/$package/CVS/Tag" ]; then + echo "W: check whether this is the correct tag: `cat $MGLTOOLSCVS/$package/CVS/Tag`" + else + echo "W: no tag file found. You may be working on the trunk, not on the release branch. Is that what you want?" + fi + sleep 3 + (cd $MGLTOOLSCVS/$package && $CVS -z3 update -d) +else + echo "I: ... now performing checkout" + (cd "$MGLTOOLSCVS" && $CVS -z3 -d$REMOTECVSROOT co -r $branch $package) +fi + +version=`echo $branch|sed "s/rc-//g"|tr '-' '.'` + +DATE=`date +"%Y%m%d"` +if [ -f $MGLTOOLSCVS/build-for-date ]; then + DATE=`cat $MGLTOOLSCVS/build-for-date` +fi +origFilename=${DEBPACKAGE}_${version}${rcversion}+cvs.${DATE}.orig.tar.gz +origDirname=${DEBPACKAGE}-${version}${rcversion}+cvs.${DATE} + +echo "I: Filename of origFile: $origFilename" + +cd "$MGLTOOLSCVS" +if [ -d "$TARDIR" ]; then + echo "I: directory for orig tarballs already available" +else + echo "I: creating directory for irog tarballs: '$TARDIR'" + mkdir "$TARDIR" +fi + +if [ -f "$TARDIR"/"$origFilename" ]; then + echo "I: delete old file '$origFilename' " + rm "$TARDIR"/"$origFilename" +fi +if [ -n "$origDirname" -a -d "$origDirname" ]; then + echo "W: Amazingly, temporary directory name '$origDirname' is already existing. Stop this script if this shall not be removed -- within 3 seconds." + sleep 3 + rm -r "$origDirname" +fi + +echo "I: Temporarily renaming and taring $package " +echo " --> $MGLTOOLSCVS/$TARDIR/$origFilename" +mv "$package" "$origDirname" +echo -n "I: Number of files in package: " +GZIP=-9 tar --exclude CVS -czvf "$TARDIR/$origFilename" "$origDirname" | wc -l +mv "$origDirname" "$package" +echo "I: done" + --- mgltools-webservices-1.5.6~rc2+cvs.20111222.orig/debian/get-orig-source/README +++ mgltools-webservices-1.5.6~rc2+cvs.20111222/debian/get-orig-source/README @@ -0,0 +1,10 @@ +This directory contains all scripts/data/whatsoever to automatically build +mgltools-packages. +Using svn externals, this directory appears in the debian directory of each +package. So in case you need to change anything (like the branch to be used), +there is only one place to make the modifications. + + +Command in trunk/debian: +svn propset svn:externals \ + '^/trunk/packages/mgltools/mgltools-external-get-orig-source get-orig-source' . --- mgltools-webservices-1.5.6~rc2+cvs.20111222.orig/debian/get-orig-source/current-branch +++ mgltools-webservices-1.5.6~rc2+cvs.20111222/debian/get-orig-source/current-branch @@ -0,0 +1 @@ +rc-1-5-6